The infant gut microbiota is the set of microorganisms colonizing the baby's intestine. This complex ecosystem appears to be related to various physiological conditions of the host and it has also been shown to act as one of the most crucial determinants of infant's health. Furthermore, the mother's endocrine system, through its hormones, can have an effect on the composition of the newborn's gut microbiota. In this perspective, we summarize the recent state of the art on the intricate relationships involving the intestinal microbiota and the endocrine system of mother/baby to underline the need to study the molecular mechanisms that appear to be involved.